Isoaspartyl dipeptidase

 

Isoaspartyl dipeptidase (IAD) from Escherichia coli is a member of the amidohydrolase superfamily. It catalyses the hydrolysis of dipeptides containing a peptide bond to the beta-carboxylate group of aspartic acid. The apparent physiological role of IAD is to prevent the accumulation of beta-aspartyl dipeptides after proteolysis of these proteins. IAD shows little activity towards the hydrolysis of tripeptides or gamma-glutamyl dipeptides.

 

Reference Protein and Structure

Sequence
P39377 UniProt (3.4.19.-) IPR033826 (Sequence Homologues) (PDB Homologues)
Biological species
Escherichia coli K-12 (Bacteria) Uniprot
PDB
1onw - Crystal structure of Isoaspartyl Dipeptidase from E. coli (1.65 Å) PDBe PDBsum 1onw
Catalytic CATH Domains
3.20.20.140 CATHdb (see all for 1onw)
Cofactors
Zinc(2+) (2) Metal MACiE
Click To Show Structure

Enzyme Reaction (EC:3.4.19.5)

beta-Asp-Leu
CHEBI:68600ChEBI
+
hydroxide
CHEBI:16234ChEBI
→
L-aspartate(1-)
CHEBI:29991ChEBI
+
leucine
CHEBI:25017ChEBI
Alternative enzyme names: Beta-aspartyl dipeptidase, Beta-aspartyl peptidase, Beta-aspartyldipeptidase,

Enzyme Mechanism

Introduction

The presence of the two Zn(II) ions lowers the pKa of a water molecule to such an extent that it exists as a hydroxide ion. The interaction between the carbonyl oxygen and Zn2 increases the electrophilic character of the carbonyl carbon atom. Asp 285 acts as a general base by abstracting the proton from the hydroxide ion, causing the oxygen atom to nucleophilically attack the substrate carbonyl carbon atom. This forms a negatively charged, tetrahedral intermediate. As the carbonyl is reformed, the scissile C-N bond is broken, facilitated by Asp 285 acting as a general acid by donating a proton to the leaving group N atom.

Catalytic Residues Roles

UniProt PDB* (1onw)
Lys162 Kcx162A Post-translationally carbamalated. Acts as a bridging ligand for both zinc ions through the carbamate group. metal ligand
His201, His230 His201A, His230A Forms part of the zinc 2 binding site. metal ligand
Asp285 Asp285A Part of the Zinc 1 binding site. Acts as a general base by abstracting a proton from the hydroxide ion, activating it further for nucleophilic attack. Acts as a general acid by donating that proton to the leaving group N atom. hydrogen bond acceptor, hydrogen bond donor, metal ligand, proton acceptor, proton donor
His68, His70 His68A, His70A Forms part of the zinc 1 binding site. metal ligand
*PDB label guide - RESx(y)B(C) - RES: Residue Name; x: Residue ID in PDB file; y: Residue ID in PDB sequence if different from PDB file; B: PDB Chain; C: Biological Assembly Chain if different from PDB. If label is "Not Found" it means this residue is not found in the reference PDB.

Chemical Components

proton transfer, bimolecular nucleophilic addition, overall reactant used, intermediate formation, unimolecular elimination by the conjugate base, intermediate collapse, intermediate terminated, overall product formed, native state of enzyme regenerated

References

  1. Martí-Arbona R et al. (2005), Biochemistry, 44, 7115-7124. Mechanism of the Reaction Catalyzed by Isoaspartyl Dipeptidase fromEscherichia coli†,‡. DOI:10.1021/bi050008r. PMID:15882050.
  2. Zhang HM et al. (2015), J Chem Theory Comput, 11, 2525-2535. Include dispersion in quantum chemical modeling of enzymatic reactions: the case of isoaspartyl dipeptidase. DOI:10.1021/acs.jctc.5b00246. PMID:26575552.
  3. Thoden JB et al. (2003), Biochemistry, 42, 4874-4882. High-resolution X-ray structure of isoaspartyl dipeptidase from Escherichia coli. DOI:10.1021/bi034233p. PMID:12718528.

Step 1. Asp285 deprotonates the zinc activated hydroxide group. This then attacks the carbonyl carbon of the peptide bond in a nucleophilic addition.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Asp285A hydrogen bond acceptor, metal ligand
Kcx162A metal ligand
His70A metal ligand
His68A metal ligand
His230A metal ligand
His201A metal ligand
Asp285A proton acceptor

Chemical Components

proton transfer, ingold: bimolecular nucleophilic addition, overall reactant used, intermediate formation

Step 2. The oxyanion initiates an elimination that cleaves the peptide bond. The amine side of the bond then deprotonates Asp285.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Asp285A hydrogen bond donor
Asp285A metal ligand
Kcx162A metal ligand
His70A metal ligand
His68A metal ligand
His230A metal ligand
His201A metal ligand
Asp285A proton donor

Chemical Components

proton transfer, ingold: unimolecular elimination by the conjugate base, intermediate collapse, intermediate terminated, overall product formed, native state of enzyme regenerated
Download: Image, Marvin File

Step 1. Asp285 deprotonates the zinc activated hydroxide group. This then attacks the carbonyl carbon of the peptide bond in a nucleophilic addition.

Step 2. The oxyanion initiates an elimination that cleaves the peptide bond. The amine side of the bond then deprotonates Asp285.

Products.

Contributors

Gemma L. Holliday, Daniel E. Almonacid, Ellie Wright, Charity Hornby